EOM to model flexible C-terminus on dimeric protein

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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sepley
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EOM to model flexible C-terminus on dimeric protein

#1 Post by sepley » 2017.11.27 17:45

I was trying to use EOM for the first time.
I would like to model the flexible C-termini on a dimeric protein of 254 amino acids. (I have a crystal structure showing the dimer formed by the first 125 amino acids for each monomer).
I have tried providing EOM a pdb containing the dimer, or 2 monomers (keeping them fixed) and a sequence file containing the entire sequence. In both cases I get an error message
Number of residues per chain: 254
Alignment Problems: check the sequence and the domains

What is the correct input format?

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AL
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Re: EOM to model flexible C-terminus on dimeric protein

#2 Post by AL » 2017.12.07 14:17

sepley wrote:Number of residues per chain: 254
Alignment Problems: check the sequence and the domains
Please run pdb2seq on your crystal structure - this will give you the sequence. Note that in case of a dimer you will get the same sequence twice. Please compare it in a text editor to the sequence provided to EOM - the folded domain sequence must be a substring of the full sequence.

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